I can confirm that in your save, the comfy beds are visible, except for one that the inventory says it’s undeployed, but it’s nowhere to be found, there’s not in a backpack or the ground, nor in storage.
Thanks for the info, @Gaddiel 
Edit: I got this bug while trying to reproduce another one. However, I was able to see the only item in my stockpile, being able to place it with the button on the unit frame, so it might be a different instance of the bug.
My steps:
1-Start a game and build a tiny cottage.
2-Use the Clear tool in game, dragging a square that encloses the bed inside the cottage (and at least one wall).
3-Make another bed (it will replace the one in the cottage automatically, due to the recent feature).
4-Undeploy the bed.
5-Place the bed again inside the cottage.
6-Undeploy the bed again.
7-Look at the Place item menu, the bed won’t appear there.
Uh-oh, if I tell the hearthlings to remove the building now, it will play the destruction effect in a loop 
Can anyone reproduce it with these steps? I have many mods installed so it might be just me. 
(It’s probably the Clear tool that shouldn’t be able to remove building parts)…